Data presented below was generated and/or compiled from several sources:
sample_metrics_data: sample annotation (e.g., donor ID, timepoint, etc.) as well sequencing & alignment metrics from RNA-seq processingsample_rapmap_data: read coverage measured across the length of the CAR transcript, based on mapping with the RapMap toolsample_salmon_data: abundance estimates (e.g., TPM, count) produced by the Salmon tool for CAR and several relevant transcripts when mapping to a modified human reference transcriptome (hg38)salmon_imgt_data: predicted/identified TCR junction sequences and alleles in single-cell libraries, as produced by assembly with Trinity followed by matching with IMGT High V-QUESTload("data/sample_metrics_data.RData")
load("data/sample_rapmap_data.RData")
load("data/sample_salmon_data.RData")
load("data/sample_tcr_data.RData")
gff_file <- "data/annotation/carPlus.gtf"
xcripts_gtf <- import.gff2(gff_file)
median_cv_coverage < 1mapped_reads_w_dups > 0.7log2(TPM +1) > 0 for CAR transcript
## Source: local data frame [6 x 3]
## Groups: car_expr_tpm [?]
##
## car_expr_tpm nz_cov n_distinct(lib_id)
## (chr) (lgl) (int)
## 1 car_expr_tpm FALSE 18
## 2 car_expr_tpm TRUE 55
## 3 car_expr_tpm NA 1
## 4 no_car_tpm FALSE 444
## 5 no_car_tpm TRUE 37
## 6 no_car_tpm NA 4
log2(TPM + 1) >= 2.5 in any of CAR or EGFRt transcripts OR log2(TPM + 1) > 2 in all CAR or EGFRt transcripts
## Source: local data frame [6 x 3]
## Groups: car_expr_quant [?]
##
## car_expr_quant nz_cov n_distinct(lib_id)
## (chr) (lgl) (int)
## 1 car_expr_quant FALSE 107
## 2 car_expr_quant TRUE 58
## 3 car_expr_quant NA 2
## 4 no_car_quant FALSE 355
## 5 no_car_quant TRUE 34
## 6 no_car_quant NA 3
= 10 positions with > 0 reads in ANY of CD19scFv, T2A, or EGFRt
## Source: local data frame [5 x 3]
## Groups: car_expr_cov [?]
##
## car_expr_cov nz_cov n_distinct(lib_id)
## (chr) (lgl) (int)
## 1 car_expr_cov FALSE 2
## 2 car_expr_cov TRUE 53
## 3 no_car_cov FALSE 460
## 4 no_car_cov TRUE 39
## 5 NA NA 5